PDBsum entry 2asj

Transferase/DNA

PDB id: 2asj

Contents

Protein chains

341 a.a. *

DNA/RNA

Metals

_CA ×3

Waters ×144

* Residue conservation analysis

PDB id:

2asj

Name:

Transferase/DNA

Title:

Oxog-modified preinsertion binary complex

Structure:

5'-d( Gp Gp Tp Tp Gp Gp Ap Tp Gp Gp Tp Ap (Ddg))-3'. Chain: d, h. Engineered: yes. Other_details: primer strand (dideoxy-terminated at 3'-end). 5'-d( Cp Tp Ap Ap Cp (8Og) Cp Tp Ap Cp Cp Ap Tp Cp Cp Ap Ap Cp C)-3'. Chain: e, j. Engineered: yes. Other_details: oxog-modified template strand.

Source:

Synthetic: yes. Sulfolobus solfataricus. Organism_taxid: 2287. Gene: dbh, dpo4. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.35Å R-factor: 0.249 R-free: 0.318

Authors:

O.Rechkoblit,L.Malinina,Y.Cheng,V.Kuryavyi,S.Broyde,N.E.Geacintov, D.J.Patel

Key ref:

O.Rechkoblit et al. (2006). Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. Plos Biol, 4, e11-18. PubMed id: 16379496

Date:

23-Aug-05 Release date: 10-Jan-06

Protein chains

Q97W02  (DPO4_SULSO) -  DNA polymerase IV from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 352 a.a.

Struc: 341 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-G-T-T-G-G-A-T-G-G-T-A-DDG 13 bases

C-T-A-C-C-A-T-C-C-A-A-C-C 13 bases

G-G-T-T-G-G-A-T-G-G-T-A-DDG 13 bases

C-T-A-C-C-A-T-C-C-A-A-C-C 13 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Plos Biol 4:e11-18 (2006)

PubMed id: 16379496

Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion.

O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geacintov, D.J.Patel.

ABSTRACT

7,8-dihydro-8-oxoguanine (oxoG), the predominant lesion formed following oxidative damage of DNA by reactive oxygen species, is processed differently by replicative and bypass polymerases. Our kinetic primer extension studies demonstrate that the bypass polymerase Dpo4 preferentially inserts C opposite oxoG, and also preferentially extends from the oxoG*C base pair, thus achieving error-free bypass of this lesion. We have determined the crystal structures of preinsertion binary, insertion ternary, and postinsertion binary complexes of oxoG-modified template-primer DNA and Dpo4. These structures provide insights into the translocation mechanics of the bypass polymerase during a complete cycle of nucleotide incorporation. Specifically, during noncovalent dCTP insertion opposite oxoG (or G), the little-finger domain-DNA phosphate contacts translocate by one nucleotide step, while the thumb domain-DNA phosphate contacts remain fixed. By contrast, during the nucleotidyl transfer reaction that covalently incorporates C opposite oxoG, the thumb-domain-phosphate contacts are translocated by one nucleotide step, while the little-finger contacts with phosphate groups remain fixed. These stepwise conformational transitions accompanying nucleoside triphosphate binding and covalent nucleobase incorporation during a full replication cycle of Dpo4-catalyzed bypass of the oxoG lesion are distinct from the translocation events in replicative polymerases.